Symmetry breaking of single-walled carbon nanotubes (SWNTs) has profound effects on their optoelectronic properties that are essential for fundamental study and applications. Here, we show that isomeric SWNTs that exhibit identical photoluminescence (PL) undergo symmetry breaking by flavin mononucleotide (FMN) and exhibit dual PLs and different binding affinities (Ka). Increasing the FMN concentration leads to systematic PL shifts of SWNTs according to structural modality and handedness due to symmetry breaking. Density gradient ultracentrifugation using a FMN-SWNT dispersion displays PL shifts and different densities according to SWNT handedness. Using the optical titration method to determine the PL-based Ka of SWNTs against an achiral surfactant as a titrant, left- and right-handed SWNTs display two-step PL inflection corresponding to respective Ka values with FMN, which leads to the determination of the enantiomeric excess (ee) of the SWNT ensemble that was confirmed by circular dichroism measurement. Decreasing the FMN concentration for the SWNT dispersion leads to enantiomeric selection of SWNTs. The titration-based ee determination of the widely used sodium cholate-based SWNT dispersion was also demonstrated by using FMN as a cosurfactant.